Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
Name
s41467-021-25279-y.pdf
Description
Published version
Size
5.32 MB
Format
Adobe PDF
Checksum (MD5)
4ca363b3b78f1c6047e678799a769347
Author(s)
Genshaft, Alex S
Ziegler, Carly GK
Tzouanas, Constantine N
Mead, Benjamin E
Jaeger, Alex M
Navia, Andrew W
King, Ryan P
Mana, Miyeko D
Huang, Siyi
Mitsialis, Vanessa
Date Issued
2021
Journal
Nature Communications
Publisher
Springer Science and Business Media LLC
Citation
Genshaft, Alex S, Ziegler, Carly GK, Tzouanas, Constantine N, Mead, Benjamin E, Jaeger, Alex M et al. 2021. "Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes." Nature Communications, 12 (1).
Version
Final published version
Abstract
AbstractA cell’s phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT—Spatially PhotoActivatable Color Encoded Cell Address Tags—to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
Massachusetts Institute of Technology. Department of Chemistry
Koch Institute for Integrative Cancer Research at MIT
Ragon Institute of MGH, MIT and Harvard
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Department of Biology
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1038/S41467-021-25279-Y
